Re: [R] Grouped Boxplot

2014-07-14 Thread S Ellison
I want to plot boxplots in such a way that DISO is on y-axis and the NODE_CAT is grouped according to POS. If I were to plot the above mentioned case I should get three groups of boxplots A, B, and C. Also each of the POS A, B and C should have two boxplots (one for Hubs and one for Nonhubs).

Re: [R] Zeta-squared transformation use R?

2014-07-14 Thread Michael Dewey
At 18:14 13/07/2014, jlh.membership wrote: Hi Miles, If I read the paper correctly, zeta-squared is simply: (1+z^2) for z=0, and 1/(1+z^2) for z=0, where z is the z-score (Eqn. 11 in the paper). Z-scores can be calculated in R using the scale(...) function. So this should produce a

Re: [R] Cutting hierarchical cluster tree at specific height fails

2014-07-14 Thread Johannes Radinger
Of course, manually checking the number of clusters that are cut at a specific height (e.g. by abline()) is one possibility. However, this only makes sense for single trees, but is not a feasible approach for multiple model runs when hundreds of trees are built with many cluster branches. Thus,

Re: [R] Scatterplot3D in r

2014-07-14 Thread Uwe Ligges
On 13.07.2014 20:30, Babak Bastan wrote: I would like to visualize my data in a scatterplot3d On my X and Y axis, I would like the same labels. Something like this: x-c(A, B, c, D) y-c(A, B, c, D) on the Z axis, I would like to show the comparison between labels in X and Y A with A A

Re: [R] Correlating multiple effect sizes within a study to study-level predictors: metafor package

2014-07-14 Thread Michael Dewey
At 23:18 11/07/2014, Megan Bartlett wrote: Hi everyone, Since metafor doesn't have its own list, I hope this is the correct place for this posting- my apologies if there is a more appropriate list. metafor questions welcome here, Megan Wolfgang seems to be off-list so while we wait for the

Re: [R] Correlating multiple effect sizes within a study to study-level predictors: metafor package

2014-07-14 Thread Viechtbauer Wolfgang (STAT)
Somehow that initial post slipped under the radar for me ... Yes, I would give the same suggestion as Michael. Besides random effects for 'site', I would also suggest to add random effects for each estimates (as in a regular random-effects model). So, if you have an 'id' variable that is unique

[R] Multiple Correspondence Analysis

2014-07-14 Thread Abhinaba Roy
Hi R-helpers, I am using 'mjca' in the package 'ca' to perform multiple correspondence analysis. However the number of factor variables is large (n = 35) and CA_actRem$nd.max[1] 14 How do I interpret the results? what is the best way to identify the similar factors and levels as the plot is

[R] sqldf problems

2014-07-14 Thread Juan Daniel García
Hello: I'm trying to run this code data2 - sqldf ( SELECT plot, age, avg(N) as N FROM data1 GROUP BY plot, t) The problem is that when calling sqldf with require(sqldf) appears this message Warning message: In sqliteCloseConnection(conn, ...) : RS-DBI driver warning: (closing pending result

[R] R] R GUI for undergraduate lab class?

2014-07-14 Thread Dr. Thomas W. MacFarland
Hi Louise: Pasted below is a section from a syllabus where I list a set of Tegrity-based URLs that demonstrate the R Commander Graphical User Interface, for R-based analyses and graphics. The videos are all about 1 hour in length but there is a slider at the bottom so it is fairly easy to

Re: [R] sqldf problems

2014-07-14 Thread Gabor Grothendieck
2014-07-14 7:52 GMT-04:00 Juan Daniel García juandaniel...@gmail.com: Hello: I'm trying to run this code data2 - sqldf ( SELECT plot, age, avg(N) as N FROM data1 GROUP BY plot, t) The problem is that when calling sqldf with require(sqldf) appears this message Warning message: In

Re: [R] sqldf problems

2014-07-14 Thread Jeff Newmiller
One doesn't call a package... so your description is unclear. One doesn't load (using the require or library functions) the relevant package AFTER calling functions in the package. Since it appears you have left out some steps or described them out of order, please supply a reproducible example

Re: [R] R GUI for undergraduate lab class?

2014-07-14 Thread john verzani
Ranjan Maitra maitra.mbox.ignored at inbox.com writes: Hi Louise, The INZight GUI might give students something to work with. https://www.stat.auckland.ac.nz/~wild/iNZight/ __ R-help@r-project.org mailing list

Re: [R] Merge rows

2014-07-14 Thread David Stevens
Cautionary note on the solution below. Be sure the 'sndr' is either factor or character because, if sndr is numeric, as the list is populated, R will fill in non-adjacent list items with NULLs, leaving a list with many empty entries. So, the modified line is

[R] two questions - function help and 32vs64 bit sessions

2014-07-14 Thread Fowler, Mark
Hello, Two unrelated questions, and neither urgent. Windows 7, R 3.0.1. Using R Console, no fancy interface. The function help ultimately becomes lost to a session kept running for extended periods (days). I.e. with a new session if you invoke the Help menu 'R functions (txt)...' it

Re: [R] Zeta-squared transformation use R?

2014-07-14 Thread jlh.membership
Yes, absolutely! Sorry about that: zeta.sq - function(data) { z - scale(data) zeta.sq - ifelse(z0,1+z^2,1/(1+z^2)) } -Original Message- From: Michael Dewey [mailto:i...@aghmed.fsnet.co.uk] Sent: Monday, July 14, 2014 6:57 AM To: jlh.membership; 'Miles Yang' Cc:

Re: [R] gamm4 and lme4 error

2014-07-14 Thread Simon Wood
Thanks - It looks like an lme4 1.1-7 change. I'll look for a work around (once I can get nlopt-2.4 to install). Meanwhile, I think it's still safe to use. best, Simon On 13/07/14 05:05, Nicholas Lange wrote: Hello, I'm running R.3.1.1 on Mac OS X 10.6.8 with gamm4 version 0.2-2 and lme4

Re: [R] two questions - function help and 32vs64 bit sessions

2014-07-14 Thread Jeff Newmiller
I don't know any definitive answer for either if your questions, but I have a comment that may explain why I have not encountered these issues. At one time I used to use RData files the way you are, but I discovered the value of re-running my analysis scripts from scratch regularly... as in

[R] New details about Cochran and Cox's chocolate cake data

2014-07-14 Thread Kevin Wright
On 3 Jun 2000, Bill Venables posted (to the S-Plus email list) a very nice explanation of how to think about split-plot designs using Cochran and Cox's chocolate cake data and the lme function. A copy of that posting is here: https://biostat-lists.wustl.edu/sympa/arc/s-news/2000-06/msg00023.html

Re: [R] canonical correlation

2014-07-14 Thread Michael Friendly
Perhaps what you are looking for is the visualization methods for canonical correlation provided in the candisc package. see ?candisc::cancor ?heplot.cancor -Michael On 13/07/2014 4:39 PM, Monaly Mistry wrote: Dear John, In my final model I have 10 independent variables that account for

Re: [R] Correlating multiple effect sizes within a study to study-level predictors: metafor package

2014-07-14 Thread Megan Bartlett
Thanks very much, Wolfgang and Michael! I feel like I understand rma much more clearly. But just to make sure, is there any way to do this kind of analysis for a continuous predictor variable? For each site level, I have a value for a climate variable, and it would be great to see whether the

[R] Update fail

2014-07-14 Thread jwd
I've been getting of an R-patched update, but running the process results in the following: File './x86_64/R-patched-devel-3.1.1-4.1.x86_64.rpm' not found on medium 'http://download.opensuse.org/repositories/devel:/languages:/R:/patched/openSUSE_13.1/' The system is opensuse 13.1, Linux

Re: [R] two questions - function help and 32vs64 bit sessions

2014-07-14 Thread Jim Lemon
On Mon, 14 Jul 2014 01:42:54 PM Fowler, Mark wrote: Hello, Two unrelated questions, and neither urgent. Windows 7, R 3.0.1. Using R Console, no fancy interface. The function help ultimately becomes lost to a session kept running for extended periods (days). I.e. with a new

[R] List of Lists by for Loop

2014-07-14 Thread Munjal Patel
Dear Experts, I have a one more doubt about making list of lists. Here is the simple code i have made. I am doing the following for only one digit=20 a=vector(20,mode=list) b=vector(20,mode=list) for (i in 1:20){ #Do Calculation a[[i]]=data.frame() b[[i]]=data.frame() } Now i have

[R] how to remove outliers

2014-07-14 Thread Marta valdes lopez
Hi! I did this test and I got this outlier that i would like to remove the whole row in my database; anyone knows how i can remove it? chisq.out.test(time$TimeDiff) chi-squared test for outlier data: time$TimeDiff X-squared = 73260.07, p-value 2.2e-16 alternative hypothesis: highest

[R] Determine the order of Time series

2014-07-14 Thread 张天添
Dear R help team, I am currently stuck on how to determine the order of a data. I have plotted the ACF and PACF of the data and it does not seem to cuts off. Is that possible to plot AIC BIC of some order(p,q) say, 0p6 and 0q10 on the same graph so that I can compare the value of AIC and

[R] Dimensionality of Higher-Order Moments of rmgarch

2014-07-14 Thread dragomir nedeltchev
Hi Everybody, I wonder whether there are ways to reduce the dimensionality of calculating higher moments via rmgarch? How about real-cases when there are dozens of positions in the portfolio? Thank you. Best regards, Dragomir Nedeltchev [[alternative HTML version deleted]]

[R] List of Lists in For Loop

2014-07-14 Thread Munjal Patel
Dear Experts, I have a one more doubt about making list of lists. Here is the simple code i have made. I am doing the following for only one digit=20 a=vector(20,mode=list) b=vector(20,mode=list) for (i in 1:20){ #Do Calculation a[[i]]=data.frame() b[[i]]=data.frame() } Now i have to

[R] Mac OSX Mavericks 10.9.3 Big Problem - New User

2014-07-14 Thread Ryan Dallavia
Hello, I am new to this program. I initially installed both R and R Studio 3 months ago, easily and got a d-base icon from the package I needed, and saw my tables in spreadsheet form in studio. Now, everything has disappeared on its own -seriously nothing changed. When trying to get my package

Re: [R] how to remove outliers

2014-07-14 Thread Hasan Diwan
Marta, To remove a row from your data frame, use: value - 14478.4 time - time[-time[$TimeDiff] == value,] I hope that helps... If not, do push back. -- H On 14 July 2014 09:17, Marta valdes lopez martavalde...@gmail.com wrote: Hi! I did this test and I got this outlier that i would like to

Re: [R] Mac OSX Mavericks 10.9.3 Big Problem - New User

2014-07-14 Thread Jeff Newmiller
Providing error messages without the inputs that provoked them leaves us with only half a conversation to interpret. (For instance, what is with the misspelling error?) It is also helpful when they are provided in the sequence that they happened. I am going to make a wild guess that you loaded

Re: [R-es] outliers (Marta valdes lopez)

2014-07-14 Thread Javier Villacampa González
Hola Marta, si observas cualquier artículo de psicología esto es una práctica típica. Te digo psicología porque creo que tus datos son de ese tipo. Tienes bibiligrafía de artículos cientificos en las que se quitan valores siguiendo los criterios que te he dicho solo has de buscar

Re: [R-es] outliers (Marta valdes lopez)

2014-07-14 Thread Marta valdes lopez
Hola de nuevo, Ya esta solucionado era cualquier error en el archivo que ya corregi. Muchas gracias, un saludo El 14 de julio de 2014, 16:40, Marta valdes lopez martavalde...@gmail.com escribió: Hola, Si entiendo lo que quieres decirme, el problema es que hago lo que tu haces y me sale